U.S. officials believe terrorists linked to al-Qaida may be plotting new attacks targeting Americans.
The advisory was prompted by the outbreak of hostilities in Aceh province, where Indonesian forces have battled separatists.
The State Department says soft targets are particularly vulnerable.
They include, "hotels, clubs, restaurants, shopping centers, housing compounds, transportation systems, places of worship, schools or outdoor recreation events."
The statement supersedes the one issued April 25, which also warned Americans against nonessential travel to Indonesia.